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FF:10044-101F8: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 16:29, 29 March 2012


Name:spleen, fetal, pool1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissuespleen
dev stage12-31 weeks fetus
sexmixed
ageNA
cell typeCELL MIXTURE - tissue sample
cell lineNA
companyClontech
collaborationFANTOM5 OSC CORE (contact: Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot number3040796
catalog numberCat:636585
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.141
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood2.052811e-5
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
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C87-retinoblastoma-left-nonsmall-heart-small-diaphragm-bronchogenic0
C88-Melanocyte-melanoma-Macrophage-Mesenchymal-migratory-Dendritic-Monocytederived0
C89-small-retinoblastoma-medulloblastoma-iPS-acantholytic-eye-bronchogenic0
C9-skeletal-diaphragm-tongue-throat-penis-heart-left0
C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0.0768
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0.0996
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10651

Jaspar motifP-value
MA0002.20.0596
MA0003.10.064
MA0004.10.786
MA0006.10.372
MA0007.10.747
MA0009.10.695
MA0014.10.48
MA0017.10.612
MA0018.20.321
MA0019.10.0288
MA0024.10.86
MA0025.10.151
MA0027.10.615
MA0028.10.0727
MA0029.10.432
MA0030.13.38285e-4
MA0031.10.0256
MA0035.28.99135e-5
MA0038.10.0611
MA0039.20.0788
MA0040.10.131
MA0041.10.15
MA0042.10.154
MA0043.10.673
MA0046.17.0815e-5
MA0047.20.0318
MA0048.10.0304
MA0050.11.09671e-8
MA0051.12.29752e-4
MA0052.12.7598e-5
MA0055.10.00456
MA0057.10.84
MA0058.10.988
MA0059.10.0154
MA0060.10.0564
MA0061.10.694
MA0062.20.534
MA0065.20.0814
MA0066.10.0785
MA0067.10.578
MA0068.13.00183e-4
MA0069.10.349
MA0070.10.252
MA0071.10.246
MA0072.10.264
MA0073.10.841
MA0074.10.383
MA0076.10.42
MA0077.10.408
MA0078.10.49
MA0079.20.0127
MA0080.25.30507e-15
MA0081.16.02527e-4
MA0083.10.13
MA0084.10.855
MA0087.10.182
MA0088.10.17
MA0090.10.702
MA0091.10.671
MA0092.10.939
MA0093.10.853
MA0099.21.32402e-7
MA0100.10.663
MA0101.10.202
MA0102.20.372
MA0103.10.108
MA0104.20.0275
MA0105.10.00428
MA0106.10.00833
MA0107.10.115
MA0108.22.22834e-14
MA0111.10.62
MA0112.20.0941
MA0113.10.907
MA0114.10.166
MA0115.10.233
MA0116.10.0567
MA0117.10.58
MA0119.10.0623
MA0122.10.069
MA0124.10.988
MA0125.10.4
MA0131.10.663
MA0135.10.0587
MA0136.14.00606e-14
MA0137.21.13006e-6
MA0138.20.377
MA0139.10.0996
MA0140.12.29674e-6
MA0141.10.269
MA0142.10.947
MA0143.10.507
MA0144.10.00312
MA0145.10.399
MA0146.10.796
MA0147.10.0206
MA0148.10.602
MA0149.10.179
MA0150.10.016
MA0152.10.982
MA0153.10.228
MA0154.10.694
MA0155.10.133
MA0156.17.46699e-13
MA0157.10.261
MA0159.10.223
MA0160.10.425
MA0162.10.34
MA0163.11.55949e-4
MA0164.10.505
MA0258.10.129
MA0259.10.0892



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs10651

Novel motifP-value
10.0127
100.0166
1000.0303
1010.718
1020.768
1030.336
1040.518
1050.1
1060.854
1070.648
1080.442
1090.12
110.25
1100.286
1110.0481
1120.846
1130.15
1140.031
1150.789
1160.104
1170.032
1180.0578
1190.169
120.549
1200.219
1210.103
1220.167
1230.0372
1240.565
1250.256
1260.953
1270.974
1280.95
1290.183
130.0709
1300.274
1310.264
1320.875
1330.125
1340.344
1350.148
1360.776
1370.363
1380.915
1390.216
140.743
1400.156
1410.303
1420.508
1430.732
1440.82
1450.726
1460.352
1470.234
1480.0916
1490.654
150.0987
1500.714
1510.848
1520.234
1530.57
1540.225
1550.732
1560.476
1570.9
1580.634
1590.632
160.151
1600.95
1610.948
1620.945
1630.792
1640.0104
1650.604
1660.629
1670.00183
1680.0659
1690.617
170.637
180.2
190.719
20.177
200.141
210.463
220.603
230.708
240.702
250.655
260.0533
270.476
280.804
290.0307
30.274
300.0809
310.934
320.566
330.385
340.0501
350.243
360.199
370.165
380.929
390.94
40.617
400.319
410.905
420.451
430.41
440.364
450.192
460.177
470.121
480.317
490.254
50.317
500.427
510.879
520.435
530.64
540.788
550.347
560.872
570.0369
580.951
590.369
60.51
600.82
610.573
620.635
630.547
640.27
650.931
660.71
670.59
680.869
690.487
70.784
700.00305
710.0289
720.496
730.26
740.169
750.0429
760.0326
770.785
780.377
790.238
80.14
802.05596e-4
810.419
820.419
830.84
840.621
850.738
860.724
870.735
880.617
890.327
90.211
900.0594
910.876
920.561
930.903
940.251
950.175
960.621
970.896
980.124
990.944



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs10651


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

UBERON: Anatomy
0000042 (serous membrane)
0000061 (anatomical structure)
0000062 (organ)
0000064 (organ part)
0000077 (mixed endoderm/mesoderm-derived structure)
0000464 (anatomical space)
0000465 (material anatomical entity)
0000466 (immaterial anatomical entity)
0000467 (anatomical system)
0000468 (multi-cellular organism)
0000475 (organism subdivision)
0000479 (tissue)
0000480 (anatomical group)
0000481 (multi-tissue structure)
0000916 (abdomen)
0000922 (embryo)
0000923 (germ layer)
0000925 (endoderm)
0000926 (mesoderm)
0000945 (stomach)
0001007 (digestive system)
0001041 (foregut)
0001048 (primordium)
0001062 (anatomical entity)
0001555 (digestive tract)
0002050 (embryonic structure)
0002075 (viscus)
0002095 (mesentery)
0002100 (trunk)
0002106 (spleen)
0002193 (hemolymphoid system)
0002323 (body cavity)
0002390 (hematopoietic system)
0002405 (immune system)
0002417 (abdominal segment of trunk)
0002532 (epiblast (generic))
0002553 (anatomical cavity)
0003081 (lateral plate mesoderm)
0003104 (mesenchyme)
0003281 (mesentery of stomach)
0004119 (endoderm-derived structure)
0004120 (mesoderm-derived structure)
0004177 (hemopoietic organ)
0004185 (endodermal part of digestive tract)
0004457 (cavity lining)
0004458 (body cavity or lining)
0004782 (gastrointestinal system serosa)
0004854 (gastrointestinal system mesentery)
0004872 (splanchnic layer of lateral plate mesoderm)
0004921 (subdivision of digestive tract)
0004923 (organ component layer)
0005057 (immune organ)
0005172 (abdomen element)
0005173 (abdominal segment element)
0005177 (trunk region element)
0005409 (gastrointestinal system)
0005423 (developing anatomical structure)
0005602 (dorsal mesogastrium)
0006293 (spleen primordium)
0007026 (primitive gut)
0009034 (stomach region)
0009142 (entire embryonic mesenchyme)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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